Variant report

Variant	rs6504411
Chromosome Location	chr17:46672154-46672155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr17:46669362-46676749	IMR90	lung:	n/a	chr17:46669880-46669890 chr17:46671209-46671222 chr17:46671209-46671222 chr17:46669884-46669894 chr17:46673053-46673063
2	REST	chr17:46671334-46672252	PANC-1	pancreas:	n/a	n/a
3	SIN3AK20	chr17:46670500-46672191	PANC-1	pancreas:	n/a	n/a
4	CTBP2	chr17:46671319-46673025	H1-hESC	embryonic stem cell:	n/a	n/a
5	SUZ12	chr17:46670436-46673044	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr17:46670331-46675986	PANC-1	pancreas:	n/a	n/a
7	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
8	SUZ12	chr17:46669440-46680361	NT2-D1	testis:	n/a	n/a
9	MXI1	chr17:46670335-46673027	IMR90	lung:	n/a	n/a
10	TCF7L2	chr17:46671229-46672791	PANC-1	pancreas:	n/a	chr17:46671659-46671673 chr17:46671661-46671670
11	TCF12	chr17:46671190-46672199	A549	lung:	n/a	n/a
12	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr17:46671195-46673088	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr17:46670513-46672579	IMR90	lung:	n/a	n/a
15	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46422046..46424668-chr17:46671390..46673476,2	K562	blood:
2	chr17:46664818..46667926-chr17:46672135..46673972,3	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS3	TF binding region
HOXB3	TF binding region
HOXB5	TF binding region
ENSG00000141293	Chromatin interaction
ENSG00000233101	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2288276	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288277	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2288279	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2555109	0.96[ASN][1000 genomes]
rs2740752	0.89[ASN][1000 genomes]
rs4646992	0.81[AFR][1000 genomes]
rs7405452	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7406170	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7406324	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7406910	0.82[ASN][1000 genomes]
rs890431	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9221	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9903182	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9907987	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
2	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
3	chr17:46669000-46672200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:46669200-46672400	Active TSS	Fetal Kidney	kidney
5	chr17:46669200-46672400	Active TSS	NHLF	lung
6	chr17:46670000-46672200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:46671000-46672400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:46671000-46672600	Enhancers	HUVEC	blood vessel
9	chr17:46671000-46673400	Weak transcription	Pancreas	Pancrea
10	chr17:46671000-46676200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:46671200-46673000	Genic enhancers	Rectal Mucosa Donor 31	rectum
12	chr17:46671200-46674600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr17:46671400-46673600	Weak transcription	Right Atrium	heart
14	chr17:46671400-46674200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:46671400-46674600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr17:46671600-46672200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
17	chr17:46671600-46672200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:46671600-46672200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr17:46671600-46672600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:46671600-46672600	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr17:46671600-46672800	Bivalent Enhancer	Placenta	Placenta
22	chr17:46671600-46673000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
23	chr17:46671600-46673600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr17:46671600-46675600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:46671800-46672200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:46671800-46672200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
27	chr17:46671800-46672200	Enhancers	A549	lung
28	chr17:46671800-46672400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr17:46671800-46672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:46671800-46672600	Flanking Active TSS	Colonic Mucosa	Colon
31	chr17:46671800-46672800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:46671800-46673400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:46671800-46674200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:46671800-46676200	Weak transcription	K562	blood
35	chr17:46672000-46672200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
36	chr17:46672000-46672200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr17:46672000-46672200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:46672000-46672200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:46672000-46672200	Enhancers	Adipose Nuclei	Adipose
40	chr17:46672000-46672200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
41	chr17:46672000-46672200	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr17:46672000-46672400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:46672000-46672400	Bivalent/Poised TSS	Fetal Lung	lung
44	chr17:46672000-46672400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
45	chr17:46672000-46672600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
46	chr17:46672000-46672600	Enhancers	HSMM	muscle
47	chr17:46672000-46673200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr17:46672000-46673200	Bivalent Enhancer	Fetal Intestine Large	intestine
49	chr17:46672000-46673600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:46672000-46673600	Weak transcription	HSMMtube	muscle

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